James,
You would need to send me access to a) FTP b) database and c) Gibbon interface. Is this OK? If so, Skype IM me the details.
Ross
For anyone else with this issue, it turns out that the host set the max_input_vars for the domain, and but this setting did not carry through to the sub domain where Gibbon was installed. For some reason (yet to be determined), the Manage Permission page did not correctly detect that max_input_vars was too low (which it should), and so let the user update the permissions: some of the data went missing because max_input_vars was too low, and the result was incorrect permissions.
A check is to use phpinfo (http://php.net/manual/en/function.phpinfo.php) on the subdomain in question to check if max_input_vars is correctly set (a value of 5000-10000 should be fine for most installs, but might not be enough if you have a lot of extra roles or modules).